A description of the patterns in spatial variability of fish assemblages is particularly relevant to guarantee an adequate management of these marine resources. Thirty six trawls were considered on six seagrass meadows (10 km apart) in three islands (100 km apart) of the Canary Islands to (i) analyze the spatial variability in the structure (richness, abundance and diversity) of fish assemblages associated with Cymodocea nodosa seagrass meadows, and to (ii) assess how the structural complexity of this habitat affects fish assemblage structure. A total of 3,616 fishes were captured, belonging to 30 species and 15 families. The total length of ca. 95% of individuals was < 10 cm, and ca. 90% of individuals were juveniles. Spatial variability in fish assemblage structure was larger when considering the scale of meadows than the scale of islands (27.28% vs. 6.64% respectively, in the amount of explained total variability); the smallest spatial scale (i.e., the variability among replicated trawls within each seagrass meadow) accumulated the largest amount of variability (66.07%). Differences in fish assemblage structure were largely driven by changes in the abundance of a few species, including Diplodus annularis, Spondyliosoma cantharus, Mullus surmuletus and Symphodus trutta. These species recruited into seagrass meadows, and confirmed the nursery role of this habitat in the canarian coastal waters. Mean shoot density and variation of the seagrass canopy height were the descriptors that accounted for the most variability when explaining patterns in fish assemblage structure.